Research Interests

The goals of the Laboratory of Microbial Genomics and Systems/Synthetic Biology (MGSSB) are to understand model microbes and microbial communities at the levels of molecules to systems, and to utilize that knowledge and insight to design synthetic biological parts and systems for enhanced performance.

We use genomics tools to unravel genotype–phenotype relationships and population dynamics in the laboratory and in natural environments such as oceans, soils, plants and animals, including humans. Research on individual organisms ranges from comparative genome analysis, which involves genome sequencing and annotation, to systems-level multi-omics analysis of the transcriptome and phenome.

Comparative evolutionary studies of commensal and pathogenic Escherichia coli and Shigella suggest lifestyle-specific gene contents and genomic configurations. Multi-omics analysis of the two model cell factories, E. coli B and K-12, offers baseline information for synthetic biology and next-generation biotechnology. Analysis of genomes from a long-term evolution experiment revealed that the coupling between genomic and adaptive evolution is complex and can be counterintuitive.

Because the sustainability of ecosystems depends on biodiversity, examining the structure and dynamics of their biotic constituents and grasping their genetic and metabolic capabilities are pivotal. Host physiology can be fully understood only if its microbial counterparts, pathogenic or probiotic, are appreciated. We apply high-throughput sequencing to barcode microbiota and to decode the full gene complements of metagenomes and microbiomes.

Microbiome & Metagenome

Human, plant and environmental microbial communities and their links to health, disease resistance and ecosystems.

Metagenomics circumvents the inability to cultivate most microbes and lets us study the genomic diversity of communities from the human body to extreme environments. Amplicon (16S/18S rRNA) analysis reveals community composition, and whole-metagenome analysis reveals gene content as well as community members.

We study the rhizosphere microbiome of tomato cultivars resistant or susceptible to bacterial wilt, marine microbial communities under ocean acidification and warming, and the human gut and oral microbiome in inflammatory bowel disease, gastric and colorectal cancer, and aging. We also develop large-scale analysis tools such as metaFun.

Microbial Genomics

Genome sequencing, comparative and functional genomics of bacteria from the clinic, soil, plants and the sea.

We determine genome sequences of bacteria and carry out comparative and functional genomics, integrating other omics data with the genomic information. Escherichia coli is our model for bacterial genetics and for use as a cell factory; genomes of E. coli from experimental evolution showed how genome evolution and adaptation relate (Barrick et al., Nature 2009).

We also analyze genomes of marine and soil bacteria, including a novel rhodopsin discovered in Nonlabens (Donghaeana) dokdonensis from the East Sea around Dokdo, and genomes of plant-associated bacteria that underpin plant–microbe interactions in the rhizosphere and phyllosphere.

Systems Biology

Multi-omics and computational analysis of how microbial systems behave and evolve.

Advances in sequencing and information technology let us study biological processes at the systems level. We use computational biology and bioinformatics to explore the information written in transcriptomes and metabolic networks, and how those molecular activities evolve.

Our empirical work includes experimental evolution of bacteria, phylogenetic analyses of conserved genes and studies of metabolic processes that shape gene gain and loss; our theoretical work combines experiments and computational simulations to estimate evolutionary processes.

Synthetic Biology

Engineering E. coli cell factories with redesigned chromosomes and faster growth.

Can we make a smarter cell? We combine science and engineering to design and build new biological functions and systems, using E. coli as a model. We study the genetic and phenotypic consequences of reconstructing the E. coli chromosome, for example adding replication origins to accelerate growth and biomass production.

Inspired by bacteria with multiple chromosomes such as Vibrio natriegens, which doubles in under 10 minutes, we investigate general design principles by combining experimental, theoretical and computational approaches. We also develop CRISPR-based diagnostics for plant pathogens.

Genome Evolution

Why genomes differ: adaptation, regulatory evolution and metabolic network evolution.

We analyze genome sequences and build tools to understand the evolutionary origin of genes, genomes and organisms. Projects characterize E. coli and its relatives as models for evolutionary processes, explore the role of gene families in adaptation to different environments, the impact of regulatory evolution on divergence (especially in pathogens), and how system-scale metabolic networks evolve.